I don't think you can meaningfully measure percentage completion on a project like this. It's not like (say) the projects distributed.net promotes, where there's a well-defined target. With Folding, the results learned from existing WUs guide future investigations, i.e. they determine what types of WUs they issue down the road. It's an open-ended sort of thing.
The shutdown of my Folding clients was a pragmatic decision, driven by the hot weather this past spring/summer and the cost of electricity (hot weather is especially problematic because Folding increases the load on the A/C as well, so you get hit on the electricity costs twice). With the huge improvements over the past few years in CPU and GPU power management, the "if the system is going to be on anyway you might as well put the cycles to good use" argument doesn't carry as much weight either, since the system consumes significantly less power when it is idling.
With the arrival of colder weather I will be turning a few systems back on, since the additional electricity usage will be helping to heat my house instead of fighting with my A/C.
I'll probably turn the client on my work desktop back on as well. I moved to another area about a months ago, and this area is on the same cold air feed as the data center next door. As a result we actually have to run the heat (which is electric) in here to maintain reasonable temperatures even in the summer, so that electricity would be getting used anyhow. (Yes, I agree that's goofy... but I did not design the climate control systems on this floor, I just have to live with them!) This is in contrast to my old office, where it was always too hot...
I still believe in the overall goals of the Folding@home project, but my participation lately has been tempered by practical considerations.
If the world isn't making sense to you, you're either drinking too much or not drinking enough.